Place red bell pepper and onion in a large frying pan over medium heat. Add olive oil. Cook and stir until onion becomes translucent, about 5 minutes. Add eggplant and squash; cover and cook until tender, about 5 minutes more. Add pinto beans and capers. Cook until heated through, about 5 minutes. Add rice. Stir well and add mustard seeds, garlic, pepper flakes, cumin, cilantro, and salt.